eRankPPI Datasets

eRankPPI is an algorithm for the identification of near-native conformations generated by protein docking using experimental structures as well as protein models. The scoring function implemented in eRankPPI employs multiple features including interface probability estimates calculated by eFindSitePPI and a novel contact-based symmetry score.
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If you use eRankPPI, please cite the following papers:

eRankPPI is available as a standalone software distribution.

eRankPPI is free of charge under the terms of GNU General Public License for non-commercial use. It is distributed without any warranty, but with best wishes.



In the Model ranking and selection section, you can find the non-redundant sets of crystal structures as well as high- and moderate-quality models of proteins included in the BM1755 (homo-dimers) and BM58 (hetero-dimers) datasets. In addition, we provide ZDOCK output files and numerical scores assigned to individual dimer models by ZDOCK, ZRANK and eRankPPI. The format of the results in the "Model ranking" subsection is as follows:

  1. MODEL keyword
  2. Model rank assigned by ZDOCK
  3. iRMSD [Å]
  4. Pairwise Contact Score (CMS)
  5. ZDOCK score
  6. ZRANK score
  7. eRankPPI score

In the Scoring of protein-protein interactions section, you can find the results from FiberDock applied to dimer models constructed by ZDOCK and eRankPPI for a dataset of 3,218 real hetero-dimers (HET3218, positives) and a dataset of 14,944 randomly assembled hetero-dimers (RND14944, negatives). The results include the top 10 dimer models in the PDB format as well as FiberDock output files containing various energy scores. In addition to dimer models, we provide the crystal structures of hetero-dimers (HET3218) and monomers forming homo-dimers (HOM14944). The latter were used to generate the random dataset of hetero-dimers by randomly swapping monomer proteins.

Model ranking and selection

Target proteins (BM1755, homo-dimers)
Dataset Download Size MD5  

 
Receptor crystal structures BM1755C_receptor.tar.gz 105M bb3e0bee29523095418c958db19b97ec  
Ligand crystal structures BM1755C_ligand.tar.gz 104M 23d1b728787fc5540e272cd9b063997c  
High-quality receptor models BM1755H_receptor.tar.gz 105M 490ff3e1c8f84e2b13ac3dba67be93cc  
High-quality ligand models BM1755H_ligand.tar.gz 104M 9ef653ca139c331f4d831a4848a16d57  
Moderate-quality receptor models BM1755M_receptor.tar.gz 105M 89c08a2b6ae87206bb42a79e3ce20d60  
Moderate-quality ligand models BM1755M_ligand.tar.gz 104M 5883075b0a585fd6f068e8f5a0cfd1cc  
ZDOCK output (BM1755, homo-dimers)
Dataset Download Size MD5  

 
Target crystal structures BM1755C_zdock.tar.gz 39M 3cbf92610e041ee9d230fdec071e122b  
High-quality target models BM1755H_zdock.tar.gz 39M 011c109a77023c19fd0d331004bb0e1a  
Moderate-quality target models BM1755M_zdock.tar.gz 39M e42fc0682c0730a780332baf2a27557d  
Model ranking (BM1755, homo-dimers)
Dataset Download Size MD5  

 
Target crystal structures BM1755C_results.tar.gz 65M 3a7e8293175cb8296d5daebf1b571c9e  
High-quality target models BM1755H_results.tar.gz 65M 0f520bf334788cecdff08bb8097d57ec  
Moderate-quality target models BM1755M_results.tar.gz 65M ea2b453666f87fe95e1e829ce21c82c8  
Target proteins (BM58, hetero-dimers)
Dataset Download Size MD5  

 
Receptor crystal structures BM58C_receptor.tar.gz 3.5M 96ad8ecad5ea121092213175be74637e  
Ligand crystal structures BM58C_ligand.tar.gz 2.2M 06fa8a8320b3e677b647de26f38845e7  
High-quality receptor models BM58H_receptor.tar.gz 3.5M 6d4d198c06e0bd82f0ccccf2885f33c5  
High-quality ligand models BM58H_ligand.tar.gz 2.2M 83b2116bb2c0480ae2c700c6cf27de71  
Moderate-quality receptor models BM58M_receptor.tar.gz 3.5M ffdf32df2424adab06b4275d94afd41f  
Moderate-quality ligand models BM58M_ligand.tar.gz 2.2M c4fa2dc81c383565bca543067c4d9628  
ZDOCK output (BM58, hetero-dimers)
Dataset Download Size MD5  

 
Target crystal structures BM58C_zdock.tar.gz 1.3M 9127109f180473501743e5b2079b2fbc  
High-quality target models BM58H_zdock.tar.gz 1.3M b1302909aed18015a04ff510f12fe9ee  
Moderate-quality target models BM58M_zdock.tar.gz 1.3M 3ce779db99c05408995b536f61d1646d  
Model ranking (BM58, hetero-dimers)
Dataset Download Size MD5  

 
Target crystal structures BM58C_results.tar.gz 2.7M 00afb6856c1259fd1ae7c113ffb99164  
High-quality target models BM58H_results.tar.gz 2.7M 9c0720999ca5e81bb22cf55d5796d3a3  
Moderate-quality target models BM58M_results.tar.gz 2.7M 1ff886246f2a03944ca450351e699551  

Scoring of protein-protein interactions

True interactions (HET3218, hetero-dimers)
Dataset Download Size MD5  

 
Dimer crystal structures HET3218_crystal.tar.gz 173M 9b1f184313a5a96fe91f7e9cf4f2dc09  
Dimer models refined by FiberDock HET3218_fiberdock.tar.gz 1.8G 230b9355c3b09768f29f65ac01b238fc  
Random interactions (RND14944, hetero-dimers)
Dataset Download Size MD5  

 
Monomer crystal structures HOM14944_crystal.tar.gz 480M b258112a96b3d686dab3a1c63e848aa5  
Dimer models refined by FiberDock RND14944_fiberdock.tar.gz 9.7G 08e58c1f0b712c31848acdfc51cab8a6  

 

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